A low pH may be caused by poor absorption of carbohydrate or fat. 

- A stool pH below 6.0 may be the result of a rapid transit time e.g. diarrhea, loose stools. If this is the case further investigations may be required to determine the cause which could be anything from food allergy or intolerance, bacterial, viral, or parasitic infection, or irritable bowel syndrome (assuming serious bowel disorders have been ruled out previously).

- A low pH may also be the result of small bowel bacterial overgrowth (SIBO) in which numbers of normal bacteria in the small intestine are present in much higher numbers than normal. This can result from a high carbohydrate diet, low stomach acid or reduced gut immunity, and is common in chronic fatigue syndrome, fibromyalgia, and irritable bowel syndrome (IBS). For a fast transit time the underlying cause needs to be addressed and treatment therefore varies. SIBO needs to be treated with antibiotic drugs or supplements, or both, and a low carbohydrate diet adopted.

- An acidic stool can indicate a digestive problem such as lactose intolerance or a contagion such as E. coli or rotavirus, or overgrowth of the acid producing bacteria (such as lactic acid bacteria for instance).

- Children and some adults notice that their stools have a sickly sweet smell as the result of volatile fatty acids and the presence of undigested lactose. Low stool pH also contributes to the excoriation of perianal skin which frequently accompanies the diarrhea.

The most common causes of a high (alkaline) stool pH are deficiency of beneficial bacteria and therefore SCFAs and a diet that is lacking in fibre. This situation needs to be corrected with probiotic supplements and a high fibre diet as pathogenic microorganisms including bacteria and yeast (e.g. Candida) tend to thrive in an alkaline intestinal environment. Somes types of fibre including wheat bran, oat bran, and prebiotics such as fructooligosaccharides (FOS) appear particularly good at lowering intestinal pH. 

Slightly alkaline pH may occur in cases of secretory diarrhea without food intake, colitis, villous adenoma, and possibly with antibiotic usage (with resultant impaired colonic fermentation).

High fecal pH may be a risk factor for colorectal cancer. Intake of oat bran (75−100 g/day over a 14-day period) has been shown capable of reducing fecal pH by 0.4 units. There is evidence, however, that high fecal pH may be secondarily rather than primarily related to cancer risk.